In your personal story you will get a lot of weapons/armor pieces with visuals that are otherwise very difficult to get.

For example, I got a Kymswarden skinned greatsword and a Winged Spatha skinned sword in my personal story. Both of these skins cost over 4 gold on the auction house. They're probably Mystic Forge recipes that are currently unknown to the public. I also got a Human T3 skinned sword, which would have cost me a lot of karma to get otherwise.

Always make sure you check how much a skin is worth before you delete, or you may end up regretting it later. Also, when you're choosing your reward at the end of a mission, remember that you can right click and preview to see each item. If one of them has a rare skin that you like, then I would get it even if the stats aren't what you want, since you'll replace it with higher stat items soon anyways.